Mercurial > repos > yating-l > ucsc_pslcdnafilter

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author yating-l
date Thu, 02 Feb 2017 17:06:45 -0500
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1 Galaxy wrapper for UCSC pslCDnaFilter tool (version: v340)
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2 ==========================================================
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3 Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment.
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4
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5 parameters:
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6 -----------
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7 pslCDnaFilter parameters variable definitions by genome assembly category and type of cDNA sequence.
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8
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9 # common paramters used for all assembly categories
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10
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11 Same species:
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12 -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes
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13
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14 Across species:
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15 -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes
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16
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17 # common paramters used for local near best filtering
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18
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19 Same species:
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20 -localNearBest=0.001
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21 Across species:
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22 -localNearBest=0.010
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23
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24 # finished assemblies
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25
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26 Same species:
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27 -minId=0.95 -minCover=0.25
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28 Across species:
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29 -minId=0.35 -minCover=0.25
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30
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31 # well-ordered assemblies
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32
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33 Same species:
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34 -minId=0.95 -minCover=0.15
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35 Across species:
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36 -minId=0.35 -minCover=0.15
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37
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38 # low-coverage assemblies
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39
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40 Same species:
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41 -minId=0.94 -minAlnSize=80
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42 Across species:
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43 -minId=0.33 -minAlnSize=80
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44
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45 Reference:
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46 ++++++++++
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47 `Configuration file for GenBank RefSeq alignment process <http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/makeDb/genbank/etc/genbank.conf;h=03c4f3dcd12b48cf52feaf4d09561bf0a58ee352;hb=9447c3aa53839f2adbb3c2ef14ba8540a1dea077>`_
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48
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49
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50 Source code:
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51 -------------
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52
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53 http://hgdownload.cse.ucsc.edu/admin/exe/
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54
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55 Licence
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56 -------
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57 Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com).